Ok, so taking all of your advice we had the carb re-jetted. Since I have no idea about these things I took it and had it professionally done. A week, and $250 later, I got my baby back. They said they couldn't get rid of all of the back firing, but that it was better than it was before and that I wouldn't be shooting flames. I immediately noticed that I lost almost all of my torque and it felt like it was bogging down a lot. While taking it on extended rides we were noticing that it was STILL shooting flames. My husband also noticed that the muffler itself was glowing cherry red, not only while I'm riding, but after it's been shut off as well.
Tonight we were coming home from about an hour away and decided to take the highway (I-75). Mind you this was my first experience on the highway, so I was already nervous. We had been riding for about an 20 minutes, cruising at about 70, when the bike backfired, bogged down, then the engine cut out completely. I pulled off on the side of the highway, by myself btw since the hubby was slightly ahead of me and didn't notice that I was gone. I sat there for about a minute, tried to start the bike, and luckily it did start. I mentally told myself to put my big girl panties on and get going. The hubby had pulled off about a mile up the road, so we decided to try and keep on going. We made it the rest of the way home without any issues, aside from what has become normal backfiring, bogging down and flame throwing.
After getting home my husband took the bike out and really opened it up. He got off the bike and took some video of the flames while idling, as well as a picture of the glowing muffler which was taken after the bike had been off for about 30 seconds, which I'll post up here shortly.
Does anyone have any recommendations at this point? My thought is that it's still running too lean. I'm convinced that they did not re-jet it properly, but not being a mechanic I really have no idea what I should do next. Should I take it back and complain, or is this just the way it is? Has anyone else experienced anything like this? I'm about ready to put the stock muffler back on and suffer through the go-kart like sound.